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1.
Journal of International Oncology ; (12): 328-335, 2023.
Article in Chinese | WPRIM | ID: wpr-989566

ABSTRACT

Objective:To analyze circRNAs specifically differentially expressed in esophageal squamous cell carcinoma (ESCC) based on high-throughput sequencing data.Methods:Six patients with pathologically confirmed ESCC in Tangdu Hospital of Air Force Medical University from March 2018 to March 2019 were selected as the research subjects, among which 3 were stage Ⅰ ESCC and 3 were stage Ⅲ ESCC. High-throughput sequencing technology was used to analyze the difference in the expression of circRNA in cancer tissues and adjacent tissues of patients. GO enrichment analysis, KEGG enrichment analysis and Venn analysis were performed on differentially expressed genes. The circRNA-miRNA-mRNA network was constructed using Cytoscape software. The most significantly differentially expressed genes in cancer tissues were verified in cells and tissues, and the relationships between circRNAs and clinical pathological indicators of patients were analyzed.Results:A total of 553 differentially expressed circRNAs were screened in paracancerous tissues and cancer tissues of 3 stage Ⅰ ESCC patients, of which 413 were up-regulated and 140 were down-regulated in cancer tissues; A total of 425 differentially expressed circRNAs were screened in paracancerous tissues and cancer tissues of 3 stage Ⅲ ESCC patients, of which 276 were up-regulated and 149 were down-regulated in cancer tissues. GO enrichment analysis showed that the host genes of differential circRNAs in patients with stage Ⅰ ESCC were mainly enriched in cell cycle-related biological processes such as mitotic G 2/M transition. The host genes of differential circRNAs in patients with stage Ⅲ ESCC were mainly enriched in biological processes related to cell division and tumor development, such as mitotic spindle checkpoint and cell matrix adhesion. KEGG enrichment analysis showed that the differential circRNAs in cancer tissues of stage Ⅰ and stage Ⅲ ESCC patients were mainly enriched in cancer-related biological pathways such as cell adhesion. The results of Venn analysis showed that in stage Ⅰ ESCC patients and stage Ⅲ ESCC patients, 2 and 8 circRNAs that were only specifically expressed in paracancerous tissues and had significant differences were screened out respectively, and were only specifically expressed in cancer tissues with significant differences were 11 and 14 respectively. The circRNA-miRNA-mRNA network showed that the cancer tissue-related circRNA-miRNA-mRNA network in stage Ⅰ ESCC patients consisted of 7 circRNA nodes, 10 miRNA nodes and 28 mRNA nodes, and the cancer tissue-related circRNA-miRNA-mRNA network in stage Ⅲ ESCC patients consisted of 7 circRNA nodes, 9 miRNA nodes and 49 mRNA nodes. The most significantly differentially expressed hsa-circ-0060927 and hsa-circ-0109301 in cancer tissues of patients with stage Ⅰ ESCC and stage Ⅲ ESCC were selected for cytological and histological verification. The results showed that the relative expression levels of hsa-circ-0060927 in ESCC cell lines TE1, TE13, KYSE30, KYSE170, and human normal esophageal epithelial cell line HEEC were 7.82±1.96, 12.69±2.68, 12.78±2.74, 7.53±1.75, and 2.43±0.17, respectively, with a statistically significant difference ( F=4.68, P=0.004). The relative expression levels of hsa-circ-0060927 in ESCC cell lines TE1, TE13, KYSE30, and KYSE170 were higher than that in human normal esophageal epithelial cell line HEEC, with statistically significant differences ( P=0.009; P=0.003; P=0.003; P=0.007). The relative expression levels of hsa-circ-0109301 in ESCC cell lines TE1, TE13, KYSE30, KYSE170, and human normal esophageal epithelial cell line HEEC were 5.16±1.32, 6.28±1.57, 4.89±1.13, 8.92±2.12, and 22.56±4.13, respectively, with a statistically significant difference ( F=4.31, P=0.022). The relative expression levels of hsa-circ-0109301 in ESCC cell lines TE1, TE13, KYSE30, and KYSE170 were lower than that in human normal esophageal epithelial cell line HEEC, with statistically significant differences ( P=0.027; P=0.015; P=0.024; P=0.008). The expression level of hsa-circ-0060927 in cancer tissues of 13 early ESCC patients was 12.89±2.67, significantly higher than 5.73±1.18 in paracancerous tissue, and there was a statistically significant difference ( t=15.02, P<0.001) ; the expression level of hsa-circ-0109301 in cancer tissues of 19 patients with advanced ESCC was 7.78±2.17, significantly lower than 16.32±3.15 in paracancerous tissue, and there was a statistically significant difference ( t=9.73, P<0.001). The expression of hsa-circ-0109301 was related to the degree of tumor differentiation in advanced ESCC patients ( P=0.023) . Conclusion:One circRNA (hsa-circ-0060927 and hsa-circ-0109301) with the most significanty differential expression is selected in early and advanced ESCC patients respectively, in which hsa-circ-0060927 is highly expressed in ESCC cancer tissues and hsa-circ-0109301 is lowly expressed in ESCC cancer tissues, and the expression of hsa-circ-0109301 is correlated with the degree of tumor differentiation.

2.
Journal of International Oncology ; (12): 745-748, 2022.
Article in Chinese | WPRIM | ID: wpr-989508

ABSTRACT

Single-cell RNA-seq (scRNA-seq) can describe the changes of gene expression in a single tumor cell. And it can reveal the status and function of tumor cells, and capture the extensive transcriptome heterogeneity in the cell population. The application of scRNA-seq can monitor the specific highly expressed genes in esophageal squamous cell carcinoma (ESCC) , and it can also monitor genes related to radio chemotherapy resistance in tumor cells, which is helpful to provide more accurate auxiliary diagnosis for ESCC. Besides, scRNA-seq can evaluate the recurrence risk and survival time of patients. An in-depth study of the relationship between tumor cells and tumor microenvironment in ESCC will provide a theoretical basis for developing a new immunotherapy scheme for ESCC.

3.
Journal of Leukemia & Lymphoma ; (12): 480-483, 2022.
Article in Chinese | WPRIM | ID: wpr-953989

ABSTRACT

Objective:To investigate the molecular genetic and clinical characteristics of MEF2D-BCL9 fusion gene-positive acute B-cell lymphoblastic leukemia (B-ALL), and to provide the reference for the diagnosis and treatment of the disease.Methods:The medical record and experimental examination data of a 18-year-old female MEF2D-BCL9 fusion gene-positive B-ALL patient were retrospectively analyzed. The clinical manifestations and biological characteristics of MEF2D-BCL9 fusion gene-positive B-ALL were summarized.Results:This 18-year-old female patient was treated in a local hospital in December 2018 and was diagnosed as B-ALL. She achieved complete remission after chemotherapy and recurred at 6 months after the initial onset, and then she was admitted to Hebei Yanda Ludaopei Hospital in the 9 months after the initial onset.MEF2D-BCL9 fusion gene was detected through RNA-sequencing (RNA-seq) and verified by using polymerase chain reaction and Sanger sequencing. Bone marrow cell morphology was similar to mature B cells with vacuoles but without characteristic chromosome karyotype abnormalities. The patient achieved remission after VLD regimen chemotherapy, chimeric antigen receptor T-cell (CAR-T) therapy and bridged to allogeneic hematopoietic stem cell transplantation (allo-HSCT). She has maintained complete remission for 2 years at the last follow-up in February 2022.Conclusions:MEF2D-BCL9 fusion gene-positive B-ALL is characterized with high risk, early relapse and poor prognosis. These patients may benefit from CAR-T and allo-HSCT. It further emphasizes the importance of taking MEF2D-BCL9 fusion gene into the detection or identification by using RNA-seq, particularly for those newly diagnosed B-ALL patients in children and adolescents with specific bone marrow morphology.

4.
J. appl. oral sci ; 28: e20200242, 2020. tab, graf
Article in English | LILACS, BBO | ID: biblio-1134786

ABSTRACT

Abstract Heterogeneous cell populations of osteo/cementoblastic (O/C) or fibroblastic phenotypes constitute the periodontal dental ligament (PDL). A better understanding of these PDL cell subpopulations is essential to propose regenerative approaches based on a sound biological rationale. Objective Our study aimed to clarify the differential transcriptome profile of PDL cells poised to differentiate into the O/C cell lineage. Methodology To characterize periodontal-derived cells with distinct differentiation capacities, single-cell-derived clones were isolated from adult human PDL progenitor cells and their potential to differentiate into osteo/cementoblastic (O/C) phenotype (C-O clones) or fibroblastic phenotype (C-F clones) was assessed in vitro. The transcriptome profile of the clonal cell lines in standard medium cultivation was evaluated using next-generation sequencing technology (RNA-seq). Over 230 differentially expressed genes (DEG) were identified, in which C-O clones showed a higher number of upregulated genes (193) and 42 downregulated genes. Results The upregulated genes were associated with the Cadherin and Wnt signaling pathways as well as annotated biological processes, including "anatomical structure development" and "cell adhesion." Both transcriptome and RT-qPCR showed up-regulation of WNT2, WNT16, and WIF1 in C-O clones. Conclusions This comprehensive transcriptomic assessment of human PDL progenitor cells revealed that expression of transcripts related to the biological process "anatomical structure development," Cadherin signaling, and Wnt signaling can identify PDL cells with a higher potential to commit to the O/C phenotype. A better understanding of these pathways and their function in O/C differentiation will help to improve protocols for periodontal regenerative therapies.


Subject(s)
Humans , Adult , Osteoblasts/cytology , Periodontal Ligament/surgery , Dental Cementum/cytology , Cadherins/metabolism , Cell Differentiation , Cells, Cultured , Clone Cells , Transcriptome
5.
The Korean Journal of Internal Medicine ; : 178-183, 2019.
Article in English | WPRIM | ID: wpr-719454

ABSTRACT

BACKGROUND/AIMS: To evaluate and select microRNAs relevant to acute myeloid leukemia (AML) pathogenesis, we analyzed differential microRNA expression by quantitative small RNA next-generation sequencing using duplicate marrow samples from individual AML patients. METHODS: For this study, we obtained paired marrow samples at two different time points (initial diagnosis and first complete remission status) in patients with AML. Bone marrow microRNAs were profiled by next-generation small RNA sequencing. Quantification of microRNA expression was performed by counting aligned reads to microRNA genes. RESULTS: Among 38 samples (32 paired samples from 16 AML patients and 6 normal marrow controls), 27 were eligible for sequencing. Small RNA sequencing showed that 12 microRNAs were selectively expressed at higher levels in AML patients than in normal controls. Among these 12 microRNAs, mir-181, mir-221, and mir-3154 were more highly expressed at initial AML diagnosis as compared to first complete remission. Significant correlations were found between higher expression levels of mir-221, mir-146, and mir-155 and higher marrow blast counts. CONCLUSIONS: Our results demonstrate that mir-221 and mir-181 are selectively enriched in AML marrow and reflect disease activity. mir-3154 is a novel microRNA that is relevant to AML but needs further validation.


Subject(s)
Humans , Bone Marrow , Diagnosis , Leukemia, Myeloid, Acute , MicroRNAs , RNA , Sequence Analysis, RNA
6.
Chinese Journal of Dermatology ; (12): 506-509, 2019.
Article in Chinese | WPRIM | ID: wpr-755790

ABSTRACT

Single-cell RNA sequencing is a method for transcriptome profiling at the single-cell level,and is a hotspot technology in the field of biological research currently.Compared with the common high-throughput RNA sequencing,single-cell RNA sequencing can distinguish the biological differences between single cells,and identify rare cell populations and subpopulations.This review mainly describes the single-cell RNA sequencing method,summarizes current application of this technique in the field of dermatology,and discusses limitations and prospects of this technique.

7.
Biomolecules & Therapeutics ; : 290-297, 2018.
Article in English | WPRIM | ID: wpr-714737

ABSTRACT

We aimed to understand the molecular changes in host cells that accompany infection by the seasonal influenza A H1N1 virus because the initial response rapidly changes owing to the fact that the virus has a robust initial propagation phase. Human epithelial alveolar A549 cells were infected and total RNA was extracted at 30 min, 1 h, 2 h, 4 h, 8 h, 24 h, and 48 h post infection (h.p.i.). The differentially expressed host genes were clustered into two distinct sets of genes as the infection progressed over time. The patterns of expression were significantly different at the early stages of infection. One of the responses showed roles similar to those associated with the enrichment gene sets to known ‘gp120 pathway in HIV.’ This gene set contains genes known to play roles in preventing the progress of apoptosis, which infected cells undergo as a response to viral infection. The other gene set showed enrichment of ‘Drug Metabolism Enzymes (DMEs).’ The identification of two distinct gene sets indicates that the virus regulates the cell's mechanisms to create a favorable environment for its stable replication and protection of gene metabolites within 8 h.


Subject(s)
Humans , Apoptosis , Epithelial Cells , Gene Expression Regulation , High-Throughput Nucleotide Sequencing , Influenza A Virus, H1N1 Subtype , Influenza, Human , Lung , Metabolism , RNA , Seasons
8.
Genomics & Informatics ; : 51-53, 2017.
Article in English | WPRIM | ID: wpr-69978

ABSTRACT

High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy. Numerous bioconductor packages have been developed for the statistical analysis of RNA-Seq data. However, these tools focus on specific aspects of the data analysis pipeline, and are difficult to appropriately integrate with one another due to their disparate data structures and processing methods. They also lack visualization methods to confirm the integrity of the data and the process. In this paper, we propose an R-based RNA-Seq analysis pipeline called TRAPR, an integrated tool that facilitates the statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, the filtering of low-quality data, normalization, transformation, statistical analysis, data visualization, and result visualization that allow researchers to build customized analysis pipelines.


Subject(s)
Base Sequence , Gene Expression , Gene Expression Profiling , Molecular Sequence Data , Programming Languages , Sequence Analysis, RNA , Statistics as Topic , Transcriptome
9.
International Neurourology Journal ; : S76-S83, 2016.
Article in English | WPRIM | ID: wpr-55826

ABSTRACT

This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields. De novo genome assembly and large scale DNA resequencing to understand genomic variations are popular genomic research tools for processing a tremendous amount of data at low cost. Studies on transcriptomes are now available, from previous-hybridization based microarray methods. Epigenetic studies are also available with NGS applications such as whole genome methylation sequencing and chromatin immunoprecipitation followed by sequencing. Human genetics has faced a new paradigm of research and medical genomics by sequencing technologies since the Human Genome Project. The trend of NGS technologies in human genomics has brought a new era of WGS by enabling the building of human genomes databases and providing appropriate human reference genomes, which is a necessary component of personalized medicine and precision medicine.


Subject(s)
Humans , Chromatin Immunoprecipitation , Computational Biology , DNA , Epigenomics , Genetics, Medical , Genome , Genome, Human , Genomics , High-Throughput Nucleotide Sequencing , Human Genome Project , Methylation , Precision Medicine , Sequence Analysis, RNA , Transcriptome
10.
Tianjin Medical Journal ; (12): 47-50, 2014.
Article in Chinese | WPRIM | ID: wpr-475132

ABSTRACT

Objective To investigate the effects of nicotine on the gene expression profile in prefrontal cortex (PFC) region of rats. Methods Twenty-four adult male F344 rats were randomly divided into treatment group and control group, with 12 animals in each group. Animals in treatment group were injected with nicotine solution while those in control group were given physiological saline for 17 days. At the end of drug administration, the tissue of PFC region was sliced from the brain of each animal. RNA sequencing (RNA-Seq) was utilized to analyze the gene expression profile in PFC of each animal. Bioinformatics tools including Bowtie, Tophat and Cufflinks were used to map the sequencing reads to the reference genome of rat, and to measure the relative expression level of each transcript. Genes whose expression levels were significantly differ-ent between the two groups were identified. The functional categories and the biochemical pathways associated with these genes were further analyzed. Results By comparing the expression level of each transcript between two groups, 885 signifi-cantly differentially expressed genes were identified. These genes were enriched in multiple Gene Ontology Biological Pro-cess categories (e.g., G protein coupled receptor protein signaling pathway, protein ubiquitination, and neurotransmitter up-take) and biological pathways (e.g., insulin signaling pathway, Alzheimer's disease, and long term potentiation). Conclu-sion Nicotine treatment may regulate signaling transduction, energy metabolism and other biological processes in PFC of rat brain.

11.
Chinese Journal of Infectious Diseases ; (12): 597-599, 2011.
Article in Chinese | WPRIM | ID: wpr-423170

ABSTRACT

ObjectiveTo report the first laboratory-confirmed human monocytic ehrlichiosis (HME) case in Shandong Province.MethodsThe epidemiological investigation was done by filling out questionaires.Blood sample was collected for detecting the specific 16S rRNA gene of Anaplasma phagocytophilumandEhrlichiachaffeensisbynested-polymerasechainreaction(PCR).ResultsThis case was characterized by acute onset of fever,leukopenia and thrombocytopenia.The specific 16S rRNA gene of Anaplasma phagocytophilum was negative and the specific 16S rRNA gene of Ehrlichia chaffeensis was positive by nested PCR test.The PCR product was sequenced.The homology was above 99 % between the acquired nucleotide acid sequence and the Ehrlichia chaffeensis sequences registered in GenBank.ConclusionThe Ehrlichia chaffeensis infection exists in Shandong Province,which warrants further research on these natural loci of HME in this area.

12.
Chinese Journal of Laboratory Medicine ; (12): 814-819, 2011.
Article in Chinese | WPRIM | ID: wpr-419835

ABSTRACT

ObjectivesTo identified the strain 1012 from the National Center of Clinical Laboratory of China for microbe inter-laboratory quality assessment in 2010, and study the taxonomic status of strain 1012 and related species in the genus Actinomyces. Methods The bacterial traditional morphological characteristics, commercial API systems, and 16S rRNA gene sequence analysis were applied to identify the problematic culture of strain 1012. The phylogenetic tree based on the remote information of the prokaryotes systems was constructed to study the taxonomic status and evolutionary relationship of the genus Actinomyces and related species in the family Actinomycetaceae. Results Strain 1012 was determined as a kind of facuhative anaerobic,non-spot-forming,Gram-positive coryneformbacteria,which was identifiedto Actinomyces turicensis for the phenotypic biochemical characteristics of more than 60 items, The comparative study of 16S rRNA gene showed the strain 1012 with 99. 8% similarities to Actinomyces turicensis, but only 90. 6% to the type species of Actinomyces bovis in the genus Actinomyces. However, the comparative study of 16S rRNA gene showed the strain 1012 with only 90. 6% homology to the type species of Actinomyces bovis in the genus Actinomyces. Further phylogenetic analysis showed that nine independent clusters were grouped in the family Actinomycetaceae, of which four clusters were separately represented the genera Varibaculum,Mobiluncus, Actinobaculum and Arcanobacterium, while other five clusters all were designated to the genus Actinomyces. The study showed strain 1012 was located in genus Ⅲ of Actinomyces, yet with a relatively long genetic distance to Actinomyces bovis. ConclusionThe genus Actinomyces may be reclassified as one genus Actinomyces sensu stricto and several new genera for the genotypic characteristics.

13.
Chinese Journal of Laboratory Medicine ; (12): 41-45, 2011.
Article in Chinese | WPRIM | ID: wpr-382751

ABSTRACT

Objective To identify one runny mucoid-like Gram-negative bacteria with pink pigment isolated from clinical pus sample. Methods The pus sample was aseptically extracted from a deep lesions of one patient, then stored in Amies medium at room temperature for transportation. One sheep blood plate and one chocolate plate were used to detect the possible pathogens from the specimens. After inoculation, the plates were placed in a humidified incubator with 5% CO2 at 35 ℃. To identify the obtained isolates, we used the commercial Vitek2 and API systems, combining some traditional morphological examination and classical biochemical and physiological characteristics. For pure cultures, the cellular fatty acids were extracted, methylated, and determined by gas chromatography method. The 16S rRNA gene was amplified and sequenced by a commercial broad-spectrum PCR primers. The phylogenetic tree based on 16S rRNA gene was constructed by Mega 4.1 software using the neighbour-joining methods with 1 000 bootstrap replications. Results One runny mucoid-like Gram-negative bacterium, named K8756, was isolated both on sheep blood and chocolate plates after 72 h incubation. The API 20NE profile was 1245045 after a 3-day culture, which would be identified as Ochrobactrum anthropi with a good confidence of 98% probability. It was identified as Ralstonia pickettii and Bordetella bronchiseptica by VITEK 2 GN kits. However, further comparative 16S rRNA gene sequences showed that strain K8756 was closely related to the valid published Roseomonas mucosa MDA 5527 with 100% identity. Colonial morphologic features, phenotypic characteristics and major cellular fatty acid composition were also with high similarity to Roseomonas mucosa. Conclusions Strain K8756( = GIMCC 1.0030 ) is identified as Roseomonas mucosa by the polyphasic phenotypic and genotypic characteristics. The comparative analysis based on 16S rRNA gene sequences is a useful method for identifying the problematic and newly named bacteria.

14.
Chinese Journal of Infectious Diseases ; (12): 236-238, 2011.
Article in Chinese | WPRIM | ID: wpr-412819

ABSTRACT

Objective To identify Taenia cestodes specimens collected from Baoshan and Puer regions of Yunnan Province by analyzing mitochondrial DNA gene encoding ribosomal RNA small subunit (mtDNA-12S rRNA) gene sequence. Methods The adult Taenia cestode samples were collected from Baoshan and Puer regions of Yunnan Province. The genomic DNA was extracted and mtDNA-12S rRAN gene was amplified by polymerase chain reaction (PCR), then sequenced.Combined with the known mtDNA-12S rRNA gene sequence of Taenia solium, Taenia saginata,Taenia asiatica in GenBank, homology tree and phylogenetic tree were constructed by DNA MAN software. Results Taenia cestode homology tree and phylogenetic tree showed that gene sequences of BS1, BS2, BS4 and BS5 were most close to YZ with identity of 99% and those of BS3, BS6, BST,PE1 and PE2 were most close to ND with identity of 99%. Conclusions Taenia saginata and Taenia asiatica can be found in Baoshan area, while Taenia saginata can be found in Puer area. The gene sequence of mtDNA-12S rRNA can be used for clarifying the three types of Taenia cestode.

15.
Chinese Journal of Laboratory Medicine ; (12): 126-131, 2010.
Article in Chinese | WPRIM | ID: wpr-379965

ABSTRACT

Objective To establish a molecular technique of internal transcribed spacer (ITS) sequencing to identify pathogenic fungi species from the fungal sinusitis tissues. Methods Total 270 sinusitis tissues samples were collected by endoscopic surgery from 2006 to 2008. The histopathology, organize spring clip culturation and ITS region (ITS region region of fungal rRNA, including ITS1-5. 8S rRNA-ITS2) sequencing were employed simultaneously. And then to evaluate the ITS sequencing as the tool for identification of pathogenic fungi directly from clinical samples. Results Of the 270 samples, histopathology positive rate was 80.0% (216/270) , organize spring clip positive rate was 80.0% (216/ 270), fungal culturation positive rate was 53.0% (143/270) , ITS region sequencing positive rate was 63. 0% [ (134 +28 +8)/270], There were 22 species and 6 genera identified by fungal culturation, and 32 species identified by ITS region sequencing. Conclusion ITS region sequencing will become a applicable tool in clinical laboratory in future.

16.
Chinese Journal of Laboratory Medicine ; (12): 644-648, 2009.
Article in Chinese | WPRIM | ID: wpr-380818

ABSTRACT

Objective To compare sequence analysis of the yeast-like fungal isolates with traditional methods and analyze the feasibility of identification of common yeast-like fungal by sequence analysis of gene. Methods 115 yeast-like fungal isolates were collected in the clinical laboratory of Beijing Tongren Hospital. DNA of yeast-like fungal was extracted and then amplified with universal primers of part of 18S rRNA genes followed by sequencing directly. The sequences obtained were submitted to the GenBank (NCBI) to identify the fungi. At the same time, the CHROMagar Candida and Vitek 32 YBC were used to identify the fungi. The identification accuracy with three methods was compared to explore the feasibility of the identification of sequence analysis. Results 18S rRNA gene sequence analysis was compared with traditional method. There were some differences in the identification results of 13 strains. The coincidence rate between CHROMagar Candida and sequence analysis was 89. 2% (91/102) and the coincidence rate between Vitek 32 YBC and sequence analysis was 91.3% (105/115). The positivity rate of species-level identification by CHROMagar Candida , Vitek 32 YBC and the 18S rRNA gene sequence analysis were 88. 7 % ( 102/115 ), 100% ( 115/115 ), 100% ( 115/115 ). Conclusion Identification of medically important yeast-like fungal by sequence analysis of the 18S rRNA gene is reliability.

17.
Experimental & Molecular Medicine ; : 643-651, 2006.
Article in English | WPRIM | ID: wpr-106421

ABSTRACT

To investigate the genomic properties of HIV-1, we collected 3,081 sequences from the HIV Sequence Database. The sequences were categorized according to sampling region, country, year, subtype, gene name, and sequence and were saved in a database constructed for this study. The relative synonymous codon usage (RSCU) values of matrix, capsid, and gp120 and gp41 genes were calculated using correspondence analysis. The synonymous codon usage patterns based on the geographical regions of African countries showed broad distributions; when all the other regions, including Asia, Europe, and the Americas, were taken into account, the Asian countries tended to be divided into two groups. The sequences were clustered into nine non-CRF subtypes. Among these, subtype C showed the most distinct codon usage pattern. To determine why the codon usage patterns in Asian countries were divided into two groups for four target genes, the sequences of the isolates from the Asian countries were analyzed. As a result, the synonymous codon usage patterns among Asian countries were divided into two groups, the southern Asian countries and the other Asian countries, with subtype 01_AE being the most dominant subtype in southern Asia. In summary, the synonymous codon usage patterns among the individual HIV-1 subtypes reflect genetic variations, and this bioinformatics technique may be useful in conjunction with phylogenetic methods for predicting the evolutionary patterns of pandemic viruses.


Subject(s)
HIV-1/genetics , Gene Expression Regulation, Viral/genetics , Europe/epidemiology , Codon/genetics , Asia/epidemiology , Americas/epidemiology , Africa/epidemiology
18.
Chinese Journal of Infectious Diseases ; (12)2001.
Article in Chinese | WPRIM | ID: wpr-679144

ABSTRACT

Objective To analyze the 23S rRNA gene partial sequences of common bacteria, and establish molecular biologic techniques to identify bacteria by the difference of gene sequences. Methods Analyzing the sequences of variable region of bacterial 23S rRNA genes, primers and oligonucleotide probes were designed accordingly. Thereafter, bacteria were identified by PCR gel electrophoresis and PCR reverse hybridization. Results There exists significant sequence difference between Gram negative bacteria and Gram positive bacteria and it could be used to differentiate these 2 kinds of bacteria quickly with PCR gel electrophoresis. Meanwhile, sequence variety in different species of bacteria was also observed and PCR reverse hybridization could be used to identify different bacterial species further.Conclusions There exist significant sequence differences among 23S rRNA genes in different common bacteria. By the sequence differences, a specific, sensitive and rapid molecular biologic techniques could be established to quickly identify the pathogens of bacterial infections.

19.
Chinese Journal of Laboratory Medicine ; (12)2001.
Article in Chinese | WPRIM | ID: wpr-582139

ABSTRACT

Objectives To understand the mutations of embB genes in M. tuberculosis isolates, and to evaluate their clinical value. Method 102 clinical isolates were identified for their mycobacterial species, and then analyzed their embB genes with PCR SSCP, PCR RFLP, and PCR direct sequencing. Results Mycobacterium tuberculosis strain H 37 R v was used as a control. 102 clinical isolates all had the same 16S rDNA SSCP profiles as M. tuberculosis . Forty one drug sensitive isolates had normal embB SSCP and RFLP profiles. Of 61 ethambutol resistant isolates, 23 (37.7%) displayed abnormal embB SSCP profiles. Eight isolates had abnormal RFLP profiles. All embB mutations situated at codon 306, whose EMB MICs were more than 20 ?g/ml. Eight isolates had ATG to ATA or ATT mutations at codon 306. Thirty isolates had ATG to GTG or CTG mutations at codon 306, whose EMB MICs were more than 30 ?g/ml. Conclusions Ethabutol resistances in some M. tuberculosis isolates were due to mutations on embB genes. PCR SSCP and PCR RFLP method might become a simple and rapid diagnostic test for genotypes of M. tuberculosis ethabutol resistance.

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